Lecture 3/3 Flashcards
what makes up an operon?
one transcriptional unit with one promoter region and multiple coding regions with one termination signal
what is the difference in location between transcription in proks and euks?
- in euks it occurs in the nucleus
- since there’s no nucleus, transcription and translation can be paired in proks
- in euks transcripts must be transported out of the nucleus for translation bc proteins are made in the cytoplasm
where does transcription and translation take place in proks?
right outside the nucleoid region (but there’s no nucleus) in ribosomes
do proks have membranous organelles?
no
what is used for elongation in trancription in proks and euks
one RNA pol in proks, at least 3 rna pols in euks
what is the difference between transcription in euks and proks in terms of editing?
the euk transcript is extensively modified, whereas it is not in proks
what is used besides for promoter regions in euks for transcription?
enhancer and repressor regions
what does rna pol i do in transcription
it transcribes rRNA (ribosomal) which becomes part of the ribosome
is there a difference between rRNAs?
they are different between plants and animals
how many rna pols in animals?
3
how many rna pols in plants?
4
are rRNAs transcribed?
no, they are non-coding and become part of the ribosome
what are some of the most abundant RNAs in the cell?
rRNAs
what does rna pol ii transcribe?
mRNA, which are the protein-coding transcripts, micro RNAs (miRNAs) and telomerase RNA (which associates with the telomerase complex but isn’t transcribed into a protein)
what does rna pol iii transcribe?
tRNAs, 5S rRNA, other small RNAs (snRNAs)
what does rna pol iv transcribe and where is it found?
it transcribes 5S RNA and siRNAs (small interfering RNAs) and is only found in plants
what does termination depend on in euks?
the rna pol
which rna pols use intrinsic terminators and how does it work?
rna pol iii pauses at polyT tract, allowing hairpin formation, causing RNA pol iii complex to dissociate
which rna pols use extrinsic terminators and how does it work?
rna pol i: Myb binds DNA between clusters of rDNA genes bc there are repeats, dislodges RNA pol i from RNA with help of termination factors
rna pol ii: large CPF (cleavage & polyadenylation factor) complex cleaves RNA during processing, dislodging the RNA pol ii from continuing transcription
what is rDNA?
ribosomal DNA
what are the different modifications to ensure transport and stability outside of the nucleus?
- 5’ cap
- poly A tail
- splicing (differential splicing: alternative transcripts; trans-splicing)
why are there different modifications to ensure transport and stability outside of the nucleus?
they ensure that the transcript gets out of the nucleus and into the cytoplasm, also ensures the stability of RNA outside of the nucleus
what is the 5’ cap?
the capping enzyme adds a ‘backward’ methylated G to the 1st nucleotide of a primary transcript
what does the 5’ cap do?
it enhances nuclear transport, protects against exonuclease degradation, and provides more efficient translation – it is not transcribed
what makes the methylated G on the 5’ cap ‘backwards’
5’ to 5’ triphosphate linkage
when is the 5’ cap added?
as transcription is happening
what does the polyA tail do?
it enhances nuclear transport, mRNA stability, and protein translation (if you take away the As, the transcript becomes unstable and starts to be digested)
how is the polyA tail brought in?
the polyadenylation signal brings in a complex of proteins and then is cleaved by a ribonuclease about 10nt downstream, it then brings in polyA polymerase complex that adds on 100-250 As to the 3’ end
what is a polyadenylation signal?
AAUAAA
does the transcript include the polyA signal?
yes
when do we have a DNA-RNA hybrid?
during transcription
Why are there loop outs of DNA during transcription?
bc DNA-RNA hybrids are discontinuous, which suggests that RNA is further processed after transcription (no modification in proks)
what are the two types of sequences involved in splicing and where do you find them?
exons (in a gene’s DNA and mature RNA – expressed regions)
introns (in DNA but not in mature RNA – intervening regions)
do euks have few or many introns
many, can be 10s to 1000s of nts
what gets removed during splicing and from where?
introns from the primary transcript
where is a transcript spliced?
there are short sequences in the primary transcript that dictate where splicing occurs (splice donor and splice acceptor sites)
what is the splice donor?
GU in the intron with a purine purine before (in exon) and after
what is the splice acceptor?
AG at 3’ end with pyramidines upstream of it
what is the spliceosome made of?
5 small nuclear RNAs (snRNAs) and ~50 proteins
how does the spliceosome work?
4 of the snRNPs (small nuclear ribonucleic particles) assemble in the cytoplasm and are transported to the nucleus where the last snRNP is added
what is the order of transport for the spliceosome creation?
RNA is made in nucleus, transported out to cytoplasm where the proteins are. RNA associates with the proteins, goes back into the nucleus, and then associates with the last snRNP
what size are exons and why?
smallish, average vertebrate exon is 137 nt, as exon size increases, decreased efficiency of spliceosome
is there more or less regulation with larger introns?
more regulation
what assembles the spliceosome complex?
SMN
how many cuts are necessary to remove an intron?
2 sequential cuts
what are the cuts necessary for splicing?
5’ cleavage at splice donor site – causes lariat formation (loop of phosphodiester linkage between G&A)
3’ cleavage at splice acceptor site
what happens to the intron after it is spliced?
it is degraded
is the 5’ site the donor or acceptor site in splicing?
donor site
is the 3’ site the donor or acceptor site in splicing?
acceptor site
what is used to make the mature RNA once the second cut has been made during splicing
RNA ligase
do modifications to the transcript happen before or after transcription?
during, they occur concurrently
what is alternative splicing?
it is when transcription occurs and you can either get the regular primary transcript where all introns are cut out, or sometimes some introns are included as part of the transcript
do alternative transcripts make the same proteins as the regular primary transcript? why?
no, even though the genes are the same, the sequence is not the same after it has had alternative splicing
is alternative splicing good or bad?
good, it helps with protein diversity within our limited number of genes
what process causes protein diversification?
alternative splicing in different cell types
what is the most famous examples of alternative splicing?
the making of antibodies
what is the most common cause of cystic fibrosis?
mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene
are any of the mutations that cause CF splicing mutations?
yes, 13% of them
what is trans-splicing?
2 transcripts from 2 different genes on 2 different chromosomes (not homologous) spliced together to make a mature mRNA
is trans-splicing common?
no, but it occurs in C. elegans and a few other organisms
what must exist in order for trans-splicing to happen?
the “leader” exon
where is the 5’ cap during trans-splicing?
on the “leader” exon
is the “leader” exon translated into a protein?
no
Do euks also have a TATA box or just proks?
euks have it too, it’s 25-30 nt upstream
what are the core promoter sequences in euks?
TATA box, CAAT box, GC box
